How can I increase my encoding frame rate? I have no drops but it's choppy.

I am streaming from a 1280x720@60fps source. Ideally, I would like to output 640x360@25fps, but I am having trouble maintaining 25fps but I don't know why because I am not dropping any frames in the encoder or buffering in my upstream.
I have tried setting the auto adjust to degrade quality but it seems like that is not doing anything to boost the frame rate. It also seems like the frame rate setting is being ignored by the encoder as well as when I set it to 25fps, I can see the frame rate in the encoder log go above 25 fps in low movement scenes.
What can I do to get a more stable frame rate?
Actual upstream bandwidth is 2200Kb/s
Encoder is set to VP6, 1500Kb/s video + 128Kb/s audio
Datarate window = small
Quality = best frame rate
CPU = Phenom II x4 @ 3.0ghz
Encoder uses about 33% CPU using FME 2.5, 90% CPU using FMLE 3.2

Your camera DOES have a Firewire port. It may be called iLink, Firewire, IEEE1394 or DV.
Canon's site
See question 4.

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